Understanding how communities are structured under relatively pristine conditions is critical to understanding their ecology and evolution. In this study, we examined the structure of aquatic communities in the Torres del Paine National Park in Chilean Patagonia. Using dipnet surveys, we quantified the distribution of larval anurans and all macroinvertebrates from 81 habitats across a hydroperiod gradient (lakes, ponds, permanent wetlands, semi-permanent wetlands, and temporary wetlands). Compared to surveys conducted at similar northern latitudes that have high species richness and hydroperiod specialization, Patagonian habitats contained a dramatically lower richness with many taxa widely distributed across the hydroperiod gradient. Overall, taxonomic richness was lowest in temporary wetlands and lakes, but highest in habitats with intermediate hydroperiods. The cause of this unimodal relationship was a small decline in the prevalence of all taxa on the temporary end of the gradient (due to habitat desiccation) but a complete exclusion of several taxa on the most permanent end of the gradient (due to fish predation). These results are consistent with North American studies of aquatic communities and lend support to the hypothesized effect of disturbance on the distribution of biodiversity. The fact that most biodiversity occurs in the temporary and intermediate hydroperiods underscores the importance of managing the full range of aquatic communities rather than only concentrating on the larger and more apparent lakes.